rna_graft.cc File Reference

#include <core/scoring/rms_util.hh>
#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/rna/util.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <protocols/stepwise/modeler/align/util.hh>
#include <protocols/viewer/viewers.hh>
#include <devel/init.hh>
#include <utility/vector1.hh>
#include <iostream>
#include <sstream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>

Typedefs
using	Matrix = numeric::xyzMatrix< Real >

Functions
void	unvirtualize_phosphates (pose::Pose &pose, utility::vector1< Size > const &unvirtualize_phosphate_residues)
void	get_pose_and_numbering (std::string const &pdb_file, pose::Pose &pose, utility::vector1< Size > &resnum)
Size	find_index (Size const val, utility::vector1< Size > const &vec)
bool	is_subset (utility::vector1< Size > const &vec_sub, utility::vector1< Size >const &vec_big)
std::map< Size, Size >	calculate_res_map (utility::vector1< Size > const &superimpose_resnum, utility::vector1< Size > const &resnum1, utility::vector1< Size > const &resnum2)
void	superimpose_pdb (pose::Pose &pose1, pose::Pose &pose2, utility::vector1< Size > const &resnum1, utility::vector1< Size > const &resnum2)
void	output_superimposed_pdb (pose::Pose const &pose2, std::string const &pdb_file2)
void	graft_in_positions (pose::Pose const &pose1, pose::Pose &pose_target, utility::vector1< Size > const &resnum1, utility::vector1< Size > const &resnum_target, utility::vector1< Size > const &resnum_graft, bool const graft_backbone_only)
void	graft_in_positions (pose::Pose const &pose1, pose::Pose &pose_target, utility::vector1< Size > const &resnum1, utility::vector1< Size > const &resnum_target)
void	close_loops (core::pose::Pose &pose, utility::vector1< Size > const &resnum)
void	graft_pdb (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< Size > const &resnum1, utility::vector1< Size > const &resnum2, pose::Pose &pose_target, utility::vector1< Size > &resnum_target)
void	rna_superimpose_and_graft_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

calculate_res_map()

std::map< Size, Size > calculate_res_map	(	utility::vector1< Size > const &	superimpose_resnum,
		utility::vector1< Size > const &	resnum1,
		utility::vector1< Size > const &	resnum2
	)

References find_index(), create_a3b_hbs::i, is_subset(), create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and runtime_assert.

Referenced by superimpose_pdb().

close_loops()

void close_loops	(	core::pose::Pose &	pose,
		utility::vector1< Size > const &	resnum
	)

References create_a3b_hbs::f, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, and predPRE::resnum.

Referenced by coarse_rna_denovo_test(), protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), protocols::abinitio::JumpSpecificAbrelax::fold(), graft_pdb(), main(), protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_fold().

find_index()

Size find_index	(	Size const	val,
		utility::vector1< Size > const &	vec
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and vec().

Referenced by calculate_res_map(), graft_in_positions(), graft_pdb(), is_subset(), and superimpose_pdb().

get_pose_and_numbering()

void get_pose_and_numbering	(	std::string const &	pdb_file,
		pose::Pose &	pose,
		utility::vector1< Size > &	resnum
	)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::rna::denovo::denovo, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::pdb_info, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and predPRE::resnum.

Referenced by rna_superimpose_and_graft_test().

graft_in_positions() [1/2]

void graft_in_positions	(	pose::Pose const &	pose1,
		pose::Pose &	pose_target,
		utility::vector1< Size > const &	resnum1,
		utility::vector1< Size > const &	resnum_target
	)

References graft_in_positions(), and test.T008_Serialization::pose1.

graft_in_positions() [2/2]

void graft_in_positions	(	pose::Pose const &	pose1,
		pose::Pose &	pose_target,
		utility::vector1< Size > const &	resnum1,
		utility::vector1< Size > const &	resnum_target,
		utility::vector1< Size > const &	resnum_graft,
		bool const	graft_backbone_only
	)

References find_index(), create_a3b_hbs::i, create_a3b_hbs::ii, test.T008_Serialization::pose1, enumerate_junctions::q, and create_a3b_hbs::r.

Referenced by graft_in_positions(), and graft_pdb().

graft_pdb()

void graft_pdb	(	pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		utility::vector1< Size > const &	resnum1,
		utility::vector1< Size > const &	resnum2,
		pose::Pose &	pose_target,
		utility::vector1< Size > &	resnum_target
	)

References basic::options::OptionKeys::chemical::chemical, close_loops(), utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, build_restypes::elem, find_index(), graft_in_positions(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, out::file::o(), option, lactamize::outfile, create_a3b_hbs::pdb_info, beta_nonlocal::pose, test.T008_Serialization::pose1, test.T008_Serialization::pose2, challenge::ss, unvirtualize_phosphates(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by rna_superimpose_and_graft_test().

is_subset()

bool is_subset	(	utility::vector1< Size > const &	vec_sub,
		utility::vector1< Size >const &	vec_big
	)

References find_index(), and kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.

Referenced by pseudoTraceRecords::addTrace(), and calculate_res_map().

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, test.T009_Exceptions::e, basic::init(), my_main(), NEW_OPT, and viewer_main().

my_main()

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, and rna_superimpose_and_graft_test().

Referenced by main().

output_superimposed_pdb()

void output_superimposed_pdb	(	pose::Pose const &	pose2,
		std::string const &	pdb_file2
	)

References utility::io::oc::cout, lactamize::outfile, make_symmdef_file_denovo::pos, test.T008_Serialization::pose2, and utility_exit_with_message.

rna_superimpose_and_graft_test()

void rna_superimpose_and_graft_test

(

)

References get_pose_and_numbering(), graft_pdb(), create_a3b_hbs::i, option, test.T008_Serialization::pose1, test.T008_Serialization::pose2, runtime_assert, in::file::s(), and superimpose_pdb().

Referenced by my_main().

superimpose_pdb()

void superimpose_pdb	(	pose::Pose &	pose1,
		pose::Pose &	pose2,
		utility::vector1< Size > const &	resnum1,
		utility::vector1< Size > const &	resnum2
	)

References calculate_res_map(), utility::io::oc::cout, find_index(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, test.T008_Serialization::pose1, test.T008_Serialization::pose2, runtime_assert, superimpose_pose(), unvirtualize_phosphates(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by rna_superimpose_and_graft_test().

unvirtualize_phosphates()

void unvirtualize_phosphates	(	pose::Pose &	pose,
		utility::vector1< Size > const &	unvirtualize_phosphate_residues
	)

References utility::vector1< T, A >::has_value(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and beta_nonlocal::pose.

Referenced by graft_pdb(), and superimpose_pdb().